Proteomic analysis of regulated dendritic cell endosomes reveals dynamic adaptation to antigen uptake and cross-presentation

ABSTRACT: MHC class I cross-presentation involves final proteolytic peptide processing by the endosomal insulin-regulated aminopeptidase (IRAP). Reasoning that analysis of the IRAP proximal proteome may inform about dynamic remodeling of a key cross-presentation compartment during antigen uptake, we developed a proximity biotinylation system by expressing a Turbo-ID-IRAP fusion protein in MuTuDCs, a cell line resembling murine type 1 conventional dendritic cells. Analysis of luminal proteins associated with IRAP at steady state and during phagocytosis revealed a massive shift upon uptake of yeast but not apoptotic cells, favoring enrichment of antigen-processing machinery, MHC class I molecules, and proteins involved in ER-associated folding and trafficking. Importantly, Sec22b modulated this proteomic landscape promoting localization of MHC-I cross-presentation proteins (e.g., MHC class I, TAP1, Wdfy4, transferrin receptor) to the IRAP environment, while its absence favored MHC-II and ER-related proteins, suggesting a Sec22b-dependent dichotomy between pathways favoring cross-presentation versus antigen degradation. Intriguingly, uptake of apoptotic cells failed to promote cross-presentation but induced two proteins related to immune tolerance, suggesting potential adaptation of proteome modulation to outcome of antigen presentation. These data suggest that IRAP+ endosomes serve as adaptive hubs integrating secretory and endocytic pathways, with Sec22b acting as a key determinant in tailoring this compartment for MHC-I-mediated cross-presentation.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Dendritic Cell

SUBMITTER: Chiara guerrera  

LAB HEAD: Ida Chiara Guerrera

PROVIDER: PXD067092 | Pride | 2026-02-09

REPOSITORIES: Pride